There is only one line feeding the sub so I’m not sure how I would connect this just to the sub.
Does the problem still occur when the sub is not operating? If so connecting the filter just to the sub won’t help very much, of course.
If the problem only occurs when the sub is operating, though, you could connect the filter between the Marantz and the sub, with a y-cable connecting the bass signal provided by the Marantz to both inputs of the filter, and with just one of the outputs of the filter connected to the sub.
The reason for the y-cable is that I see in the instructions for the filter, which I found online, that there is an "important note" saying that it should never be used with only one of its two channels connected, and "if you must do that" a y-cable should be used to connect the input signal to both inputs. I’m guessing the reason for that might have to do with the possibility that noise occurring in an unused channel as a consequence of having its input unterminated may couple into the channel that is being used. If so, a shorting plug on the unused input could be used as an alternative to a y-cable.
In any event, I agree with Lew that the filter should absolutely not be connected to the output of the cartridge. There are several reasons for that. Just to cite a couple: The hum & noise produced by the filter is specified as "> -85 db ref 1 volt." Since the 5 mv rated output of the cartridge is 46 db less than 1 volt it would mean that hum and noise produced by the filter could be as little as 85 minus 46 = 39 db below the rated output of the cartridge, which would be unlistenable. Also the unspecified and unknown input impedance of the filter stands a good chance of being too low to provide reasonable results when used with a moving magnet cartridge.
Regards,
-- Al